And I doubt bots can understand neutral ctf logic. They are pretty new to regular ctf already...

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nav_generate worked. But yeah, you're right, the bots (well except for the Snipers and Spies) just stayed in the spawn room. Is there anything I can do about this, or do I just have to wait until Valve releases support for neutral CTF?

Yeah, uh, considering there are currently 0 official maps with such a gamemode, I wouldn't expect much on that front, tbh.

You may try to trick the bots into thinking this is regular ctf by placing 2 team flags where you had your neutral flag, and having them disable each other when picked up, and maybe experiment parenting the disabled flag to the carried one too. This isn't going to be easy and there's no guarantee it will produce good results.
Basically, experiment, do without bots, or change your game mode.

FUN FACT: Once you've generated a nav, you can type nav_edit 1 in console to see the nav mesh. I'll look like a bunch of squares on the ground. You can then type nav_delete to remove whatever square is highlited in your crosshairs. Bots will only run around in the squares, so delete squares where you don't want them to go into. Type nav_save to overwrite your new nav mesh.

FUN FACT: Once you've generated a nav, you can type nav_edit 1 in console to see the nav mesh. I'll look like a bunch of squares on the ground. You can then type nav_delete to remove whatever square is highlited in your crosshairs. Bots will only run around in the squares, so delete squares where you don't want them to go into. Type nav_save to overwrite your new nav mesh.

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also useful are nav_split, nav_splice, nav_mark, nav_connect, nav_disconnect, nav_begin_area and nav_end_area. also after editing the mesh you should do nav_quicksave 0 and nav_analyze for bots to understand the navmesh better